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OPENSEQ.org
zeye2
Genes: A B A+B
Length: 348 450 732
Sequences: 12407 11952 2337
Seq/Len: 35.65 26.56 3.19
MirrorTree (Pazo et al. 2001) 0.43
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.45
2 0.00 0.01 0.90
5 0.00 0.01 1.62
10 0.01 0.02 2.36
20 0.02 0.02 2.93
100 0.15 0.02 3.36
∞ 0.19 0.06 4.38
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
159_D 137_F 0.87 0.50 0.00
48_T 126_V 0.85 0.48 0.00
34_I 370_L 0.78 0.40 0.00
216_A 204_R 0.77 0.39 0.00
307_Y 383_L 0.77 0.39 0.00
23_F 237_I 0.75 0.36 0.00
51_A 411_F 0.74 0.34 0.00
340_V 65_V 0.73 0.34 0.00
334_G 233_G 0.73 0.34 0.00
113_T 233_G 0.72 0.33 0.00
271_L 238_V 0.72 0.32 0.00
260_G 237_I 0.71 0.31 0.00
264_L 24_T 0.70 0.30 0.00
225_N 195_L 0.70 0.30 0.00
332_V 348_L 0.69 0.30 0.00
58_T 231_A 0.69 0.29 0.00
328_M 276_A 0.69 0.29 0.00
43_I 177_Q 0.69 0.29 0.00
46_A 227_W 0.67 0.27 0.00
149_I 125_L 0.67 0.27 0.00
220_Y 229_L 0.67 0.27 0.00
309_R 337_L 0.67 0.27 0.00
178_Y 24_T 0.67 0.27 0.00
146_I 342_V 0.67 0.27 0.00
264_L 348_L 0.66 0.26 0.00
19_I 215_L 0.66 0.26 0.00
39_A 118_V 0.66 0.26 0.00
308_L 272_W 0.65 0.25 0.00
23_F 193_G 0.65 0.25 0.00
159_D 209_I 0.65 0.25 0.00
42_L 362_K 0.65 0.25 0.00
19_I 161_F 0.65 0.25 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
9576 3.19 zeye2 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9575 0.08 zeye Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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